PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Pavir.1NG002100.1.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family MIKC_MADS
Protein Properties Length: 256aa    MW: 28764.8 Da    PI: 9.4545
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.1NG002100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF89.71.5e-283483251
                         ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         rie+++ rqvtfskRr+g+lKKA+ELSvLC+aeva+i+fs++g+ly ++s
  Pavir.1NG002100.1.p 34 RIEDSTSRQVTFSKRRKGLLKKAHELSVLCEAEVALIVFSPRGRLYQFAS 83
                         8***********************************************86 PP
2K-box85.31.3e-28103197599
                K-box   5 sgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaL 94 
                          ++++++e   e+++ e++ L ++i+ ++ ++R+llGe+L+s+s+keLq+Le qLe+sl++iR++K++ l++qi el+ ke++l +en +L
  Pavir.1NG002100.1.p 103 TNERVDEPGVEKWKYEATTLGQKIDAIEASKRKLLGESLGSCSIKELQELELQLENSLSSIRQRKQKKLMNQILELRDKEQKLAKENAML 192
                          4556889999******************************************************************************** PP

                K-box  95 rkkle 99 
                          r + +
  Pavir.1NG002100.1.p 193 RDQCK 197
                          *9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006629.2682585IPR002100Transcription factor, MADS-box
SMARTSM004321.4E-352584IPR002100Transcription factor, MADS-box
PROSITE patternPS0035002781IPR002100Transcription factor, MADS-box
PRINTSPR004041.0E-272747IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.07E-2927116IPR002100Transcription factor, MADS-box
PfamPF003193.0E-263481IPR002100Transcription factor, MADS-box
CDDcd002651.71E-3335100No hitNo description
PRINTSPR004041.0E-274762IPR002100Transcription factor, MADS-box
PRINTSPR004041.0E-276283IPR002100Transcription factor, MADS-box
PfamPF014861.6E-27112196IPR002487Transcription factor, K-box
PROSITE profilePS5129714.82112202IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 256 aa     Download sequence    Send to blast
MAATAAAPDQ RQIVPSDASR MRKQGRRGRR EMRRIEDSTS RQVTFSKRRK GLLKKAHELS  60
VLCEAEVALI VFSPRGRLYQ FASATDLQNT IDRYLNHTKG TPTNERVDEP GVEKWKYEAT  120
TLGQKIDAIE ASKRKLLGES LGSCSIKELQ ELELQLENSL SSIRQRKQKK LMNQILELRD  180
KEQKLAKENA MLRDQCKALP LLELNDKGHM EAATAAAGEE KEADDGRMED VETELAIGIG  240
RGRSIMDRLT SKPDC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3kov_A3e-1727113285Myocyte-specific enhancer factor 2A
3kov_B3e-1727113285Myocyte-specific enhancer factor 2A
3kov_I3e-1727113285Myocyte-specific enhancer factor 2A
3kov_J3e-1727113285Myocyte-specific enhancer factor 2A
3p57_A3e-1727113285Myocyte-specific enhancer factor 2A
3p57_B3e-1727113285Myocyte-specific enhancer factor 2A
3p57_C3e-1727113285Myocyte-specific enhancer factor 2A
3p57_D3e-1727113285Myocyte-specific enhancer factor 2A
3p57_I3e-1727113285Myocyte-specific enhancer factor 2A
3p57_J3e-1727113285Myocyte-specific enhancer factor 2A
5f28_A4e-1727113386MEF2C
5f28_B4e-1727113386MEF2C
5f28_C4e-1727113386MEF2C
5f28_D4e-1727113386MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.207900.0stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Low expression in the young panicle continues to decline as the organ mature. {ECO:0000269|PubMed:15144377, ECO:0000269|PubMed:17166135}.
UniprotTISSUE SPECIFICITY: Expressed in mature leaves and at low levels in roots and young panicles. {ECO:0000269|PubMed:15144377, ECO:0000269|PubMed:17166135}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor active in flowering time control. May control internode elongation and promote floral transition phase. May act upstream of the floral regulators MADS1, MADS14, MADS15 and MADS18 in the floral induction pathway. {ECO:0000269|PubMed:15144377, ECO:0000269|PubMed:17166135}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.1NG002100.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025806880.11e-126MADS-box protein SOC1-like isoform X2
SwissprotQ9XJ603e-62MAD50_ORYSJ; MADS-box transcription factor 50
TrEMBLA0A2S3GKP01e-121A0A2S3GKP0_9POAL; Uncharacterized protein
STRINGPavir.Aa03568.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP14133379
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G45660.17e-53AGAMOUS-like 20
Publications ? help Back to Top
  1. Thomson MJ,Edwards JD,Septiningsih EM,Harrington SE,McCouch SR
    Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL.
    Genetics, 2006. 172(4): p. 2501-14
    [PMID:16452146]
  2. Park SJ, et al.
    Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod.
    Plant J., 2008. 56(6): p. 1018-29
    [PMID:18774969]
  3. Lee S,Jeong DH,An G
    A possible working mechanism for rice SVP-group MADS-box proteins as negative regulators of brassinosteroid responses.
    Plant Signal Behav, 2008. 3(7): p. 471-4
    [PMID:19704489]
  4. Maas LF,McClung A,McCouch S
    Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice.
    Theor. Appl. Genet., 2010. 120(5): p. 895-908
    [PMID:19949767]
  5. Sun C, et al.
    The histone methyltransferase SDG724 mediates H3K36me2/3 deposition at MADS50 and RFT1 and promotes flowering in rice.
    Plant Cell, 2012. 24(8): p. 3235-47
    [PMID:22892321]
  6. Choi SC, et al.
    Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3.
    Plant Physiol., 2014. 164(3): p. 1326-37
    [PMID:24420930]
  7. Núñez-López L,Aguirre-Cruz A,Barrera-Figueroa BE,Peña-Castro JM
    Improvement of enzymatic saccharification yield in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor.
    PeerJ, 2015. 3: p. e817
    [PMID:25780769]
  8. Jin J, et al.
    MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice.
    Plant Physiol., 2015. 168(4): p. 1275-85
    [PMID:25855537]
  9. Liu X, et al.
    Brassinosteroid (BR) biosynthetic gene lhdd10 controls late heading and plant height in rice (Oryza sativa L.).
    Plant Cell Rep., 2016. 35(2): p. 357-68
    [PMID:26518431]
  10. Hwang YH, et al.
    Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time.
    Plant Cell Rep., 2016. 35(4): p. 857-65
    [PMID:26754793]
  11. Shibaya T, et al.
    Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice.
    Plant Cell Physiol., 2016. 57(9): p. 1828-38
    [PMID:27318280]
  12. Alter P, et al.
    Flowering Time-Regulated Genes in Maize Include the Transcription Factor ZmMADS1.
    Plant Physiol., 2016. 172(1): p. 389-404
    [PMID:27457125]